RT Journal
A1 de Hoon, Michiel J.L.
A1 Taft, Ryan J.
A1 Hashimoto, Takehiro
A1 Kanamori-Katayama, Mutsumi
A1 Kawaji, Hideya
A1 Kawano, Mitsuoki
A1 Kishima, Mami
A1 Lassmann, Timo
A1 Faulkner, Geoffrey J.
A1 Mattick, John S.
A1 Daub, Carsten O.
A1 Carninci, Piero
A1 Kawai, Jun
A1 Suzuki, Harukazu
A1 Hayashizaki, Yoshihide
T1 Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
JF Genome Research 
JO Genome Research 
YR 2010 
FD February 01 
VO 20 
IS 2 
SP 257 
OP 264 
DO 10.1101/gr.095273.109 
UL http://genome.cshlp.org/content/20/2/257.abstract 
AB MicroRNAs (miRNAs) are short (20–23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals.